Description

Determines the diagnostic nucleotides for each species given in
sppVector.

Usage

1

Arguments

DNAbin

An object of class 'DNAbin'.

sppVector

The species vector (see sppVector).

n

The number of pseudoreplicates to perform. Default of 100

Details

These functions provide a means for evaluating the presence of diagnostic
nucleotides that distinguish species within an alignment. nucDiag
returns the positions of bases corresponding to the definition of pure,
simple diagnostic nucleotides given by Sarkar et al (2008).

rnucDiag runs a bootstrapping-style resampling test to evaluate the
numbers of diagnostic nucleotides that might be expected by random
assortment of specimens.

Value

nucDiag returns a list giving the pure, simple diagnostic
nucleotides (i.e. those nucleotides that are fixed within species and
different from all other species) for each species in the species vector. A
result of integer(0) indicates there are no diagnostic nucleotides
for those species.

rnucDiag returns a list containing the following elements:

min

The minimum number of diagnostic nucleotides in the sample.

mean

The mean number of diagnostic nucleotides in the sample.

median

The median number of diagnostic nucleotides in the sample.

max

The maximum number of diagnostic nucleotides in the sample.

rndFreq

A list of frequency distributions of the number of diagnostic
nucleotides in groups formed by 1 sequence, 2 sequences, etc.